japan consortium for glycobiology and glycotechnology database...

Japan Consortium for Glycobiology and Glycotechnology DataBase日本糖鎖科学統合データベース

GDGDB - Glyco-Disease Genes Database The complexity of glycan metabolic pathways and the large numbers of genetic defects in these pathways make it difficult to deal with the broad range of diseases that are caused by mutations in glycan-related genes. The Glyco-Disease Genes Database (GDGDB) was created by Research Center for Glycoscience (RCMG) and released in April 2010. This database is supported by Ministry of Education, Culture, Sports, Science and Technology (MEXT) as part of Life Science Integrated Database project. At present time GDGDB provides information on about 80 genetic diseases of both glycan synthesis and degradation, and information on mutant genes that cause these diseases. In addition, we designed and created the “Pathway” and “Phenotype” ontologies for both types of these genetic diseases (Congenital Disorders of Glycosylation (CDG) and Lysosomal Storage Diseases (LSD)) and included them in the GDGDB. The Web-based user interface was created and released and now available at http://jcggdb.jp/doc/ProjectTop.action?langType=1&projectId=2.


http://acgg.asia/db/diseases/Web page in that the RDF files and the User Interfaces are provided

XML-based User Interface

GDGDB & GGDonto ontologies - RDF representation of the GDGDB data and Ontology for Genetic Diseases known to be related to Glycan Metabolism

　 Glyco-Disease Genes Database (GDGDB) was developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. Being the members of the “Life-Science Database Integration Project” of National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST), we decided to organize GDGDB information and enrich its content by integration with other biomedical resources. We designed and developed the ontologies, called GDGDB ontology and GGDonto. In addition to these ontologies, we developed a system with the user interfaces, using which the users can retrieve and search information from GDGDB and GGDonto. These XML-based and SPARQL-based user interfaces and RDF files for GDGDB ontology and GGDonto are available at http://acgg.asia/db/diseases/. We hope that these GDGDB & GGDonto ontologies with GDGDB database will help the users to better understand the etiology, pathogenesis and manifestations of the genetic diseases known to be related to glycan metabolism.


Information resources about diseases and causative genes that are used to create the classifications

RDF representation of the GDGDB data

Internal and external sources of information

GDGDB

GDGDB provides information on about 80 genetic diseases of both glycan synthesis and degradation, and information on mutant genes that cause these diseases.

We designed and developed the ontologies, called GDGDB & GGDonto ontologies . These ontologies are based on the Semantic Web Technologies and represented in Resource Description Framework (RDF) format. Using Semantic Web Approach with Web Ontology Language (OWL), Simple Knowledge Organization System (SKOS) and RDF standards, we described semantics of GDGDB data, enriched this data with additional various classifications, and linked GDGDB data with related biomedical resources.

GDGDB & GGDonto ontologies

RDF

Classifications

NCBI Databases

External information resources used to create the classifications

UMLS - Unified Medical Language SystemMeSH - Medical Subject Headings vocabulary

RDF

Link information to internal and external information resources

GlycoGene Database (GGDB)

RDF

UniProtKB_Enzymes

Information that were obtained from related information resources and included in GGDonto

NCBI Databases

RDF

GDGDB & GGDonto ontologies

Glyco-Disease Genes Database (GDGDB)

Database provided by the AIST: GDGDB provides information about genetic diseases of glycan synthesis and degradation

Database provided by the AIST: GlycoGene includes genes associated with glycan synthesis

We used the information of the enzymes that are involved in the metabolism of glycans

Database provided by the AIST:Glyco-Disease Genes Database

We used the information about diseases and causative genes

Scientific literature that are used to create the classifications of diseases by pathogenic aspects (“pathway” classifications)

Information resources that are used to create the classification of Diseases by “symptoms, signs and abnormal clinical and laboratory findings” (“phenotype” classifications)

UMLS

UMLSMeSH

Scientific literature

We used the information from Unified Medical Language System such as disease name, UMLS CUI, disease classification, and etc.

UniProtKB_Proteins

We used the information of the proteins that are product of glyco-genes


GDGDB data NCBI data: disease descriptions

GGDonto ontology NCBI data: gene descriptions

UniProtKB_Proteins UniProtKB_Enzymes

Glyco-Disease Genes Database (GDGDB)

GlycoGene Database (GGDB)

Database provided by the AIST: GlycoGene includes genes associated with glycan synthesis

Diseases:Disease names, Pathogenesis, OMIM phenotype, OMIM phenotype MIM number, and etc.

Genes:Gene name, Alias gene names, Official gene symbol, Alias gene symbol, Locus, OMIM Gene MIM number, and etc.

Diseases:Disease names, Disease definition, Data from HPO (Human Phenotype Ontology), Semantic Relations between Concepts (by using relations from UMLS), and etc.

Diseases (Congenital Disorders of Glycosylation (CDGs) and Lysosomal Storage Diseases (LSDs)):Preferred term for disease, Synonyms for disease name, UMLS CUI, Clinical findings, Semantic Relations between Concepts, and etc.

Genes:Gene names, Alias gene names, OMIM gene MIM number, NCBI Gene Id, NCBI Gene Symbol, Alias gene symbol, Locus, and etc.

Database provided by the AIST: GDGDB provides information about genetic diseases of glycan synthesis and degradation

We used the information of the enzymes that are involved in the metabolism of glycans

We used the information of the proteins that are product of glyco-genes

Features of this ontology The proposed ontology has the advantage of representing comprehensible knowledge related to genetic defects in glycan metabolism, because

it integrates the pathogenic aspects with the clinical features associated with each of these genetic disorders. The objects of these database and ontology are genetic disorders which are caused by inherent defects in single gene (single-gene

disorders). Since the information about these diseases and they causative genes have been published in a variety of medical-related information resources, the relations between this ontology and external information resources are diverse.

Structure of the GDGDB & GGDonto ontologies


Text searching

Changing the Layout of the list of DiseasesMenu for changing the layout of the list

List of Diseases

Facets sets: Faceted browsing and filtering・ Database ・ Disease Types by Metabolic Pathways・ Manifestation ・ Ontology Tree

To detailed Information about Diseases and their Causative Genes

http://acgg.asia/db/diseases/gdgdbTop Page of SPARQL-based user interface


Narrow down the subset of diseases by using the Ontology Tree

Open the “Genetic discorders of glycan syntehesis (by systems, signs and symptoms)”

Select the “(PhT_GD)※Heart Diseases”

List of diseases that are related to “(PhT_GD))※Heart Diseases”

※(PhT_GD) ： Ontology for Disorders of Glycosylation; classified by phenotype


Stanza:GGDonto: <div data-stanza=«http://acgg.asia/db/diseases/ggdonto» data-stanza-umls_cui="C2931001"></div>GDGDB: <div data-stanza=«http://acgg.asia/db/diseases/gdgdb» data-stanza-omim_id="607143"></div>Disease(NCBI): <div data-stanza="http://acgg.asia/db/diseases/gmncbi" data-stanza-umls_cui="C2931001"></div>Gene(NCBI): <div data-stanza="http://acgg.asia/db/diseases/gincbi" data-stanza-gene_id="79087"></div>Protein(UniprotKB): <div data-stanza="http://acgg.asia/db/diseases/uniprot/uniprot" data-stanza-uniprot_id="Q9BV10"></div>ENZYME(Swiss-Prot): <div data-stanza="http://acgg.asia/db/diseases/uniprot/enzyme" data-stanza-ec_number="2.4.1.260"></div>※Stanza: TogoStanza (http://www.togostanza.org/) is a generic Web framework which enables the development of reusable Web components that are embeddable

into any Web applications.

Menu items for selecting related information

Detailed Information about Diseases and their Causative Genes


GGDonto

Information about Disease from NCBI

Information about Protein from UniProtKB

Information about Enzyme from Swiss-Prot

GDGDB

Information about Gene from NCBI

Stanza provided by GGDonto

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